Pinned Repositories
10k_genomes
Various scripts for efficient processing of 10k Salmonella genomes
annogesic_scripts
running ANNOgesic for Salmonella
bioconda-recipes
Conda recipes for the bioconda channel.
D24359
data and scripts used to assemble and annotate S. Enteritidis strain D24359
D37_salmonella_paper
all the code and small data files relevant to D37712 genome + RNA-seq paper
multi-bacpipe
A convenient pipeline for processing of multi-strain bacterial RNA-Seq experiments
TRADIS
In-house pipeline for processing of TIS/TRADIS data
RMAhunter
reprocess_public_10x
Scripts to help get fastqs
STARsolo
wrapper scripts for convenient STARsolo processing of 10X and other scRNA-seq
apredeus's Repositories
apredeus/10k_genomes
Various scripts for efficient processing of 10k Salmonella genomes
apredeus/multi-bacpipe
A convenient pipeline for processing of multi-strain bacterial RNA-Seq experiments
apredeus/bioconda-recipes
Conda recipes for the bioconda channel.
apredeus/annogesic_scripts
running ANNOgesic for Salmonella
apredeus/D24359
data and scripts used to assemble and annotate S. Enteritidis strain D24359
apredeus/D37_salmonella_paper
all the code and small data files relevant to D37712 genome + RNA-seq paper
apredeus/Ent_4str
apredeus/guess_ensg
Series of scripts useful at guessing of used 10x or Ensembl/Gencode reference from a list of gene names
apredeus/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
apredeus/myodiff
Analysis and making of figures for C2C12 myodiff RNA-seq paper
apredeus/old_genequery
Old stand-alone application and web-server for GeneQuery, as well as source code for binary files. Preprocessing is available elsewhere.
apredeus/P_alcalifaciens
genome analysis of P. alcalifaciens
apredeus/rnaquant
RNA-seq quantification pipeline for eukaryotic species
apredeus/salmonella_pathways
Custom gene sets enriched in Salmonella under various in vitro and in vivo conditions
apredeus/scg_lib_structs
Collections of library structure and sequence of popular single cell genomic methods
apredeus/skater_rnaseq
Analysis of whole blood RNA-sequencing of skaters before and after exercise
apredeus/TRADIS
In-house pipeline for processing of TIS/TRADIS data
apredeus/yakutica
Analysis scripts for Gortzia yakutica paper
apredeus/apredeus.github.io
NGS bioinformatics and pipelines